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NMR Fingerprinting: Leveraging optimal control pulse design, tailored isotope labeling, and machine learning to study intractable proteins

Award Number: R01GM136859
ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 06/01/2020
PERIOD OF PERFORMANCE END DATE: 03/31/2025

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NMR Fingerprinting: Leveraging optimal control pulse design, tailored isotope labeling, and machine learning to study intractable proteins - Project summary Nuclear magnetic resonance (NMR) spectroscopy is essential for the study structure, dynamics and function of proteins in near-native conditions. NMR studies have vital implications for therapeutic development. However, as the number of amino acids in the protein increases, NMR signals decay (relax) faster, yielding lower sensitivity and resolution, while the spectrum becomes more crowded. In these cases it is challenging to match observed signals to specific nuclei in the protein (called `resonance assignment') in order to meaningfully interpret NMR data. The overarching goal of our research is to push the boundaries of NMR enabling valuable insight about the dynamics and functions of currently intractable proteins. The objective of this project is to design an NMR platform consisting of coordinated, next-generation biochemical, biophysical, mathematical, and computational techniques. Our platform is built around an original approach to NMR spectroscopy in which new information about the local environment of each nucleus is encoded in the shape and pattern of its NMR signal. The rationale is that these patterns are a `fingerprint' – an intricate and unique signature that encodes key information about which atom is responsible for each resonance peak in the NMR spectrum. We will design and realize fingerprint patterns using two innovative approaches: 1) biochemically, by selectively introducing NMR-active isotopes into carefully chosen positions in the protein samples, and biophysically, and 2) by using specialized radiofrequency pulses to accurately control the quantum interactions that determine the NMR spectrum. The resulting fingerprints will be decoded using established algorithmic structures from machine learning, notably artificial neural networks. This will facilitate automated analyses that are accessible to non-NMR specialists. Our approach to spectroscopy holds promise in the study of therapeutically important proteins expressed in eukaryotic expression systems (e.g. G-protein coupled receptors and glycosylated proteins). Current NMR data from such proteins shows clear dynamics and interactions with other proteins, but cannot yet be properly interpreted because of the difficulty of relating each NMR peak to an amino acid in the protein sequence. Our platform will deliver two significant outcomes: 1) NMR resonance assignment for meaningful analyses of previously intractable systems. 2) Enable non-NMR specialists, to easily proceed from expressing their protein sample to using NMR to study dynamics and interactions via assigned spectra. This will have a positive impact on protein science and medical research. To support our mission we have assembled a team of leading experts to test our platform with their own protein systems.


Issue Date FY	Funding FY	Legal Entity Name	Legal Entity Address	Legal Entity City	Legal Entity State	Legal Entity Zip Code	Legal Entity COUNTY	Legal Entity COUNTRY	Assistance Listing	Award Code	Budget Year	Action Date	Action Type	Action Amount

Issue Date FY: 2026 ( Subtotal = $0 )
2026	2024	DANA-FARBER CANCER INSTITUTE, INC.	450 BROOKLINE AVE	BOSTON	MA	02215	SUFFOLK	USA	Biomedical Research and Research Training	000	5	1/21/2026	NON-COMPETING CONTINUATION	$0
														Subtotal = $0

Issue Date FY: 2025 ( Subtotal = -$16,187 )
2025	2024	DANA-FARBER CANCER INSTITUTE, INC.	450 BROOKLINE AVE	BOSTON	MA	02215	SUFFOLK	USA	Biomedical Research and Research Training	000	5	8/27/2025	NON-COMPETING CONTINUATION	-$16,187
														Subtotal = -$16,187

Issue Date FY: 2024 ( Subtotal = $464,603 )
2024	2024	DANA-FARBER CANCER INSTITUTE, INC.	450 BROOKLINE AVE	BOSTON	MA	02215	SUFFOLK	USA	Biomedical Research and Research Training	000	5	5/1/2024	NON-COMPETING CONTINUATION	$464,603
														Subtotal = $464,603

Issue Date FY: 2023 ( Subtotal = $445,749 )
2023	2023	DANA-FARBER CANCER INSTITUTE, INC.	450 BROOKLINE AVE	BOSTON	MA	02115	SUFFOLK	USA	Biomedical Research and Research Training	000	4	3/30/2023	NON-COMPETING CONTINUATION	$445,749
														Subtotal = $445,749

Issue Date FY: 2022 ( Subtotal = $460,879 )
2022	2022	DANA-FARBER CANCER INSTITUTE, INC.	450 BROOKLINE AVE	BOSTON	MA	02115	SUFFOLK	USA	Biomedical Research and Research Training	001	3	5/19/2022	SUPPLEMENT FOR EXPANSION	$15,130
2022	2022	DANA-FARBER CANCER INSTITUTE, INC.	450 BROOKLINE AVE	BOSTON	MA	02115	SUFFOLK	USA	Biomedical Research and Research Training	002	3	6/29/2022	NON-COMPETING CONTINUATION	$44,577
2022	2022	DANA-FARBER CANCER INSTITUTE, INC.	450 BROOKLINE AVE	BOSTON	MA	02115	SUFFOLK	USA	Biomedical Research and Research Training	000	3	3/21/2022	NON-COMPETING CONTINUATION	$401,172
														Subtotal = $460,879

Issue Date FY: 2021 ( Subtotal = $533,999 )
2021	2021	DANA-FARBER CANCER INSTITUTE, INC.	450 BROOKLINE AVE	BOSTON	MA	02115	SUFFOLK	USA	Biomedical Research and Research Training	001	2	6/25/2021	SUPPLEMENT FOR EXPANSION	$13,250
2021	2021	DANA-FARBER CANCER INSTITUTE, INC.	450 BROOKLINE AVE	BOSTON	MA	02115	SUFFOLK	USA	Biomedical Research and Research Training	000	2	3/24/2021	NON-COMPETING CONTINUATION	$445,749
2021	2021	DANA-FARBER CANCER INSTITUTE, INC.	450 BROOKLINE AVE	BOSTON	MA	02115	SUFFOLK	USA	Biomedical Research and Research Training	002	2	7/28/2021	SUPPLEMENT FOR EXPANSION	$75,000
														Subtotal = $533,999

Issue Date FY: 2020 ( Subtotal = $495,502 )
2020	2020	DANA-FARBER CANCER INSTITUTE, INC.	450 BROOKLINE AVE	BOSTON	MA	02115	SUFFOLK	USA	Biomedical Research and Research Training	000	1	5/5/2020	NEW	$495,502
														Subtotal = $495,502

Grand Total All Awards = $2,384,545

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NMR Fingerprinting: Leveraging optimal control pulse design, tailored isotope labeling, and machine learning to study intractable proteins

Award Number: R01GM136859

ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)

PERIOD OF PERFORMANCE START DATE: 06/01/2020

PERIOD OF PERFORMANCE END DATE: 03/31/2025

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